AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00251_ecoli_reg_300.orf -o00251_ecoli_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: argQ 198 tRNA argY 198 tRNA Input sequences: #1 carA 300 carbamoyl-phosphate synthetase, glutamine (small) subunit #2 fdrA 300 involved in protein transport; multicopy suppressor of dominant negative ftsH mutants #3 ylbE 266 orf, hypothetical protein #4 nagE 300 PTS system, N-acetylglucosamine-specific enzyme IIABC #5 glnS 202 glutamine tRNA synthetase #6 aspC 184 aspartate aminotransferase #7 ompF 300 outer membrane protein 1a (Ia;b;F) #8 putA 300 proline dehydrogenase, P5C dehydrogenase #9 ycjL 121 probable amidotransferase subunit #10 ycjC 26 orf, hypothetical protein #11 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #12 goaG 37 4-aminobutyrate aminotransferase #13 gadB 300 glutamate decarboxylase isozyme #14 nadE 201 NAD synthetase, prefers NH3 over glutamine #15 gdhA 235 NADP-specific glutamate dehydrogenase #16 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #17 cvpA 165 membrane protein required for colicin V production #18 folC 69 dihydrofolate:folylpolyglutamate synthetase; dihydrofolate synthetase #19 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #20 dedA 82 orf, hypothetical protein #21 usg 65 putative PTS system enzyme II A component #22 pdxB 98 erythronate-4-phosphate dehyrogenase #23 gltX 258 glutamate tRNA synthetase, catalytic subunit #24 guaA 68 GMP synthetase (glutamine-hydrolyzing) #25 guaB 161 IMP dehydrogenase #26 b2654 300 orf, hypothetical protein #27 b2657 171 putative enzyme #28 b2658 138 orf, hypothetical protein #29 b2659 230 orf, hypothetical protein #30 gabD 22 succinate-semialdehyde dehydrogenase, NADP-dependent activity #31 gshA 72 gamma-glutamate-cysteine ligase #32 yqaB 280 putative phosphatase #33 argZ 62 tRNA #34 serV 300 tRNA #35 yqgB 120 orf, hypothetical protein #36 galP 300 galactose-proton symport of transport system #37 sprT 76 orf, hypothetical protein #38 endA 94 DNA-specific endonuclease I #39 yggJ 52 orf, hypothetical protein #40 gltB 300 glutamate synthase, large subunit #41 yhiR 202 orf, hypothetical protein #42 gor 71 glutathione oxidoreductase #43 gadA 210 glutamate decarboxylase isozyme #44 yhjA 300 putative cytochrome C peroxidase (EC 1.11.1) #45 glmS 161 L-glutamine:D-fructose-6-phosphate aminotransferase #46 glmU 300 N-acetyl glucosamine-1-phosphate uridyltransferase #47 glnA 300 glutamine synthetase #48 btuB 300 outer membrane receptor for transport of vitamin B12, E colicins, and bacteriophage BF23 #49 adiA 195 biodegradative arginine decarboxylase #50 melR 282 regulator of melibiose operon Motif number 1 TTTCTGGTTTAGCCAGTAAAAGGGAGTGATAATAAC 4 95 1 AGCCAGAAAG 0.956842 -206 TAAAGAATGTCGCCAGAAATAAACGGGCATACGGCC 11 183 1 CGCCAGAAAG 0.962522 -92 GTGTTAGATAAGCCTGGAATACATTGGGCGCTTTTT 14 34 1 AGCCTGAAAG 0.956842 -168 TGTTAGAATGCGCCCCGAACAGGATGACAGGGCGTA 17 124 1 CGCCCCAAAG 0.812455 -42 CGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTC 20 14 0 AGCCTGAAGG 0.972591 -69 ACGTAGTTACAGCCTGAAAGATGACGAGTACAAGGC 20 47 1 AGCCTGAAAG 0.956842 -36 GATAACGTTGCGCCAGCAACGGCCCGAAGGGCGAAC 32 79 1 CGCCAGAAGG 0.97625 -202 TGTTAAAACGAGCCAGCAACGTAGCGAAAGCTGTTT 38 58 0 AGCCAGAAGG 0.972591 -37 TTAATTTGATCGCCCGAACAGCAATGTTTGGGCGAT 43 11 1 CGCCCGACGG 0.917984 -200 ATTTAAATTAAGCCTGTAATGCCTTGCTTCCATTGC 43 135 1 AGCCTGAAGG 0.972591 -76 AGGCTCGGGGCGCCCGAAAAAACGGGCATACAGGTT 45 103 1 CGCCCGAAAG 0.97604 -59 CGCGCTTTACAGCCCGAAAAGGCCGGAAGATACTTG 49 135 1 AGCCCGAAGG 0.982543 -61 ****** ** * * Masking position 8 Map Score: 14.3537 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 345 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 2 TCTGCTCGTTTTTATTTCATGCAATCTTCTTG 1 41 1 TTTATTTTGC 0.731262 -260 ATTTTTTATATTATTTTGTGGCTCATGCATGT 1 132 0 TTATTTTGGC 0.82676 -169 AATTCTAACTATATTTTTTTGCCTGTCTGGAT 2 67 0 ATATTTTTGC 0.614119 -234 AGCCGTATTTTTATTTTGCTGCAAATTGTACT 4 241 0 TTATTTTTGC 0.937324 -60 CGTATGCCCGTTTATTTCTGGCGACATTCTTT 11 184 0 TTTATTTGGC 0.464764 -91 TTTTATGCTGTTATTTTTATGCGCATTCTGTG 13 95 0 TTATTTTTGC 0.937324 -206 ATAAATCCTACTTTTTTAATGCGATCCAATCA 13 263 1 CTTTTTTTGC 0.88802 -38 TCCTGGGTCATTTTTTTCTTGCTTACCGTCAC 15 126 1 TTTTTTTTGC 0.906243 -110 TCAGCGCCATTTTTATTGATGCGCGGGAAGGA 17 65 1 TTTTATTTGC 0.5633 -101 TATACGAAGTTTATTTTTATGGAGTGAAAAGT 26 44 0 TTATTTTTGG 0.655797 -257 TTAAACGCTTTTCTTTTAATGCATGGAGGTTT 27 145 0 TTCTTTTTGC 0.719677 -27 TTAAATGTTACTAATTTGTTGCTTTTGATCAC 29 195 1 CTAATTTTGC 0.775485 -36 ATCGGGAAATTTATTTTACTGCTGATATTGAT 33 41 0 TTATTTTTGC 0.937324 -22 TATAACTCAATTATTTTCATGCACTTAAATCA 36 163 1 TTATTTTTGC 0.937324 -138 ATAAATCCTACTTTTTTATTGCCTTCAAATAA 43 173 1 CTTTTTTTGC 0.88802 -38 AGGTACTGCCTTAATTTTCTGCAGACAAAAGG 46 131 1 TTAATTTTGC 0.808064 -170 CATTGAAGCACTATATTGGTGCAACATTCACA 47 116 1 CTATATTTGC 0.620832 -185 TTCGCTTTATCTTTTTTACGGCGACACGGCCA 47 222 1 CTTTTTTGGC 0.716763 -79 GACGGCTAAACTATTTTTTTGGCTGATACTGA 49 19 0 CTATTTTTGG 0.609852 -177 ******* *** Masking position 6 Map Score: 13.2265 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 172 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 3 CACTGCTCGTGCAATTGCCATGGGTGCAATTTTTAAG 2 266 1 GCGCTGGGGC 0.972661 -35 TACATCAGTGGCGCAAGCCAATGCTGCGGTTATCGAA 3 25 1 GCGCATGCGC 0.748594 -242 TTCGTCGCGCTCGTCCACACTGGCTGGATGTGCAACC 3 66 1 TCACTGGCGG 0.902243 -201 GTCATCTCCTGCCAGCGCATTGGCGGCCCGGCGTGAA 3 147 0 GCGCTGGCGC 0.994513 -120 TGCAAGACGTGAGATTGCTCTGGAAGGTATAAAAAAA 6 59 0 GAGCTGGAGG 0.70473 -126 ACAGAACTTATTGACGGCAGTGGCAGGTGTCATAAAA 7 252 1 TTGCTGGCGG 0.918308 -49 CCTTCAAGCCGCCTCTGCCTTGGCTGCGTTCGCTCCC 11 134 0 GCGCTGGCGC 0.994376 -141 GCCATCGACTTTTTATGCCTTTGCGGCATCGGGCAAT 17 15 0 TTGCTTGCGC 0.735272 -151 CATGCTCTCTGCTGTAACATTGGCAGGGAGCTTTGCT 21 20 1 GCACTGGCGG 0.966541 -46 AGAGGTGGCTTCCTCCGCGATGGGAGGAAGCTTGGGG 37 14 0 TCGCTGGGGG 0.884438 -63 GAAACGTTACGCTTTCGCGGCGGCGGCCTCTTTTCGG 41 105 1 GCGCCGGCGC 0.926404 -98 GACGTAATAGGTGCCAGCAATGGCTGCAA 42 3 0 GTGCTGGCGC 0.981191 -69 AAAGTAGGATTTATCCGCAATGGAAGCAAGGCATTAC 43 150 0 TTGCTGGAGC 0.678617 -61 GCTTTGTCTCGCAGAGACGTTTGCAGCATTCTGGAAA 44 232 1 GCACTTGCGC 0.877089 -69 ATGAGAACCAGATGCGACGTTGGCCGGCAGGTCTTCG 48 217 0 GAACTGGCGG 0.816618 -84 ** ** **** ** Masking position 8 Map Score: 11.6307 Number of sites scoring better than the average of aligned sites = 1456 Number in coding regions = 1405 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 4 ACGTTAGTTTGAATGGAAAGATGCCTGCAGACAC 7 173 1 GAGAAAGTGC 0.909398 -128 CATGGTTTTTTTTATGACACCTGCCACTGCCGTC 7 264 0 TTGACACTGC 0.611751 -37 GCAGTTAACATTTTTGAAAGGTGCAACCGCAAAA 8 95 0 TTGAAAGTGC 0.961916 -206 TTTAACATGGTTGCACAAAGTTGCAACATCATGG 8 225 1 TTCAAAGTGC 0.695008 -76 TACTCCTGTTGTTCAGAAAGGTGCAACTTAACGT 8 272 0 GTGAAAGTGC 0.981648 -29 ATGGCCTTACGTTTAGAAAGATGCCGACAACCGG 23 232 0 GTGAAAGTGC 0.981648 -27 GTATGAGCGATTTTTGACAGTTGCCTCTCCAGAC 26 121 1 TTGACAGTGC 0.879974 -180 AGCCAGCAACGTAGCGAAAGCTGTTTTGGTATGC 38 50 0 GTGAAAGTGT 0.765036 -45 AAGCTTATTGGTACAGAAATGTGCTTTAGCGCAA 40 116 0 GTGAAATTGC 0.881401 -185 CCAGAAAATTTTCCAGAATGCTGCAAACGTCTCT 44 244 0 TTGAATGTGC 0.825776 -57 GCTGCACCACGATGTGAATGTTGCACCAATATAG 47 126 0 GAGAATGTGC 0.653202 -175 GGTCGTCGTGGTAACGAAATCTGCAATTATTTTG 47 252 0 GTGAAATTGC 0.881401 -49 ACGCGCAGCGGTAAGGAAAGGTGCGATGATTGCG 48 117 1 GTGAAAGTGC 0.981648 -184 TCGCGTAATATTGATGAAACCTGCGGCATCCTTC 48 256 1 TTGAAACTGC 0.84444 -45 ** ***** *** Masking position 7 Map Score: 11.092 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 164 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 ACAGGCGTCAATCCGACCTGATTTTTTGAA 4 52 1 ATCCGACCTG 0.641758 -249 GGTAAGCGCAATGCGCCCGGCAATCTATAC 11 31 1 ATGCGCCCGG 0.966353 -244 CCGGGGATCTCTGCGCCCTGACGTTCACAA 11 218 1 CTGCGCCCTG 0.85103 -57 TTCTGTTAGAATGCGCCCCGAACAGGATGA 17 121 1 ATGCGCCCCG 0.989505 -45 TTAATGTTATATCTGCCCCGATAAAACGGG 29 12 1 ATCTGCCCCG 0.931003 -219 TAAACATATTATCTGCCCCGTTTTATCGGG 29 28 0 ATCTGCCCCG 0.931003 -203 AAAGTAATATGTGCGCCACGCAGCGACGAT 34 239 1 GTGCGCCACG 0.889494 -62 ATACGCTTTTGTGCGCCCCGAATACGGGCC 41 154 1 GTGCGCCCCG 0.990305 -49 TCCTCATCCCATGTGACCGGGTTAGCCGGC 45 16 0 ATGTGACCGG 0.723281 -146 CCGTTTTTTCGGGCGCCCCGAGCCTTGTAG 45 98 0 GGGCGCCCCG 0.950549 -64 GCGCGTGTGACCCGTCCTGAATAG 46 5 1 GTGTGACCCG 0.902885 -296 ********** Masking position 7 Map Score: 8.67242 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 287 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 6 GGGTGCAATTTTTAAGGAGTTGTT 2 287 1 TTTAAGGAGT 0.952606 -14 TATAAGGAAATCATATAAATA 7 1 1 TATAAGGAAT 0.723026 -300 AAAAGTAAAATTTAAGGAACTTTGTGAACAC 7 79 0 TTTAAGGAAT 0.948855 -222 TCAATAAAAATTTACGGAACTATTGATGAGA 7 222 0 TTTACGGAAT 0.794619 -79 CCACTACAGTTTAAGGAAATGCAAAT 10 10 1 TTTAAGGAAT 0.948855 -17 ATCCAATCATTTTAAGGAGTTTAAA 13 286 1 TTTAAGGAGT 0.952606 -15 ACGGGTTAGCTTTAAGGAAGTTTTGTCTTTT 14 164 1 TTTAAGGAAT 0.948855 -38 AGACAATAACGTTAAGGAGTTCCCT 15 5 0 GTTAAGGAGT 0.807386 -231 TGAGATATTTTTGAAGGAAATTTTTTGGAGA 32 147 0 TTGAAGGAAT 0.794619 -134 TTCAAATAAATTTAAGGAGTTCGAA 43 196 1 TTTAAGGAGT 0.952606 -15 ********* * Masking position 4 Map Score: 8.12703 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 3 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 TTGTTAATAATTCCTGTGTGATATTCATCACCTTA 2 193 1 TTCCTGTTTT 0.956333 -108 CAGGACTTTGGTCCTGTTTTTTTTATACCTTCCAG 6 42 1 GTCCTGTTTA 0.837739 -143 TTTCAGAGGATTCCTGTATGACGTTTTAACCACCA 14 96 1 TTCCTGTCTT 0.962077 -106 TTAATTTGCTTTCCTGGGTCATTTTTTTCTTGCTT 15 115 1 TTCCTGTTTT 0.956333 -121 GCGCTCCATATTCCTGCTTTATCTATATATAATGC 28 59 0 TTCCTGTTTA 0.875484 -80 AGTTATTCATTTCCTGTCTCACTTTGCCTTAATAC 29 154 1 TTCCTGTCTT 0.962077 -77 CTTTATCCATTTCCTGAATTTTCTTCTCCTTCGCC 32 192 1 TTCCTGTTTT 0.956333 -89 TTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGT 38 65 1 TTGCTGTTTT 0.681319 -30 AAACAGTCAATTCCTGACTGTCATAAAGGTGTGTT 40 13 0 TTCCTGTCTA 0.890648 -288 TCGGTATACTGTCCTGATACGCTTTTGTGCGCCCC 41 138 1 GTCCTGACTT 0.664702 -65 CGTGTGACCCGTCCTGAATAGCGTTCACATAGATC 46 14 1 GTCCTGTCTT 0.949054 -287 CCCCCCTGTTTTCCTGTTTATTCATTGATCGAAAT 46 63 1 TTCCTGTTAT 0.699752 -238 ACGCGTCCTGACTGTAATTTGAGAACGAA 46 282 0 GTCCTGTATT 0.742394 -19 ****** * * ** Masking position 5 Map Score: 7.92602 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 76 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 8 AACGAGCAGAAAAAAGTGGACCAAATGGTCAAAA 1 17 0 AAAAAGGGCA 0.955979 -284 ACAACTCCTTAAAAATTGCACCCATGGCAATTGC 2 276 0 AAAAATGCCA 0.907662 -25 AAGGTATAAAAAAAACAGGACCAAAGTCCTGTTT 6 39 0 AAAAACGGCA 0.806758 -146 CACGCTGATAAACAAGAGGACGGAAT 14 3 0 AACAAGGGCA 0.916408 -199 CACGGGCTTGAAAAAGCGCCCAATGTATTCCAGG 14 46 0 AAAAAGGCCT 0.857189 -156 GCGCATCAATAAAAATGGCGCTGAAAAAATATTC 17 55 0 AAAAATGCCA 0.907662 -111 ACTTTGGATAAAAAAGTGGTCGAACCGCGGAGTT 19 16 0 AAAAAGGGCA 0.955979 -140 GGCAACTGTCAAAAATCGCTCATACGAAACTAAT 26 112 0 AAAAATGCCA 0.907662 -189 CTGAGGACTGAACAAGGGCGCTCTTGTAAAAACA 35 49 1 AACAAGGCCT 0.751867 -72 CGAAAAGGACAACAAGGGGGCGAATCGGAGGCGC 40 273 1 AACAAGGGCA 0.916408 -28 TCCGGTAAGTAAAAATCGGCCCGTATTCGGGGCG 41 167 0 AAAAATGGCT 0.785667 -36 TTATCGTAATAAAAATCGCCCAAACATTGCTGTT 43 27 0 AAAAATGCCA 0.907662 -184 GGGGCGCCCGAAAAAACGGGCATACAGGTTGACC 45 109 1 AAAAAAGGCA 0.738001 -53 ****** ** * * Masking position 5 Map Score: 8.37169 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 57 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 9 AGTCAACTTAATGGCGGGATTTTTTATATT 1 152 0 ATGGCGGGAT 0.909289 -149 ATTTTTTTGCCTGTCTGGATCACATAATCC 2 57 0 CTGTCTGGAT 0.703828 -244 CTCGTCCACACTGGCTGGATGTGCAACCGG 3 75 1 CTGGCTGGAT 0.892095 -192 CGCCAATGCGCTGGCAGGAGATGACCGGAC 3 159 1 CTGGCAGGAG 0.954139 -108 TTTGTCTTTTCTGTCTGGAGGGGTTCA 14 185 1 CTGTCTGGAG 0.856739 -17 ATTGAGGAATCAGGCGGGAGTGATAGAATA 23 175 1 CAGGCGGGAG 0.953227 -84 GCCCGACATGAAGTCGGGCGAAGAGAA 24 8 0 AAGTCGGGCG 0.63091 -61 GCCCGACTTCATGTCGGGCGATTTATATTA 24 19 1 ATGTCGGGCG 0.841881 -50 ACGATTTTGACAGGCGGGAGGTCAAT 31 57 1 CAGGCGGGAG 0.953227 -16 CCTACACTAGCGGGATTCTTTTTGTT 39 7 1 CTAGCGGGAT 0.624271 -46 TTCTGGCCGGCTAACCCGGTCA 45 3 1 CTGGCCGGCT 0.780749 -159 TAACTTCATCATGGCAGGCGAATCTGCAGA 50 34 1 ATGGCAGGCG 0.858572 -249 TATCAGAATTATGGCAGGAGTGAGGGAGGA 50 242 0 ATGGCAGGAG 0.892095 -41 ********** Masking position 5 Map Score: 7.04366 Number of sites scoring better than the average of aligned sites = 1594 Number in coding regions = 1509 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 10 GTGCAACCGGCTTCTTCACTTATCAGCGAAC 3 95 1 CTCTTCACTT 0.704474 -172 AGGCAAAACACTGCTTCACGCCGGGCCGCCA 3 133 1 CTCTTCACGC 0.986701 -134 TCTGCTTTATGCCTGATGCGAC 5 2 1 CTCTTTATGC 0.742056 -201 TCTCTTCTTCATGCTCTCTGCTGT 21 4 1 CTCTTCATGC 0.935937 -62 GTTCGGGTTTCTACCTTACGCATTATTGTTT 23 141 0 CTCCTTACGC 0.923375 -118 CTCAAAATTTCTCCTTCACTCTATAGTCTTT 34 32 1 CTCTTCACTC 0.960499 -269 TTGTTAACCCCTACCCCACGCGTACAACCGC 39 32 1 CTCCCCACGC 0.934633 -21 AGATTTACTGCTGCTTCACGCAGGATCTGAG 50 99 0 CTCTTCACGC 0.986701 -184 CGCAGTCATCCTCCCTCACTCCTGCCATAAT 50 234 1 CTCCTCACTC 0.952509 -49 ** ******** Masking position 8 Map Score: 5.29075 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 132 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 11 TGCGCCCACGCACGCCCCTTTCATGGGTCC 3 185 0 CACGCCCCTT 0.911061 -82 TCGTTATTATCACTCCCTTTTACTGGCTAA 4 103 0 CACTCCCTTT 0.633048 -198 TCACAAAAGACACGCGTTTAATTTGCGATA 4 149 1 CACGCGTTTA 0.696816 -152 TAGCACACCTCTTTGTTAAATGC 6 4 1 CACACCTCTT 0.916069 -181 TAAATATCATCACGTCTCTATGGAAATATG 7 46 1 CACGTCTCTA 0.496278 -255 ATCGATTTAACACACCATTTACATTAAATT 8 17 1 CACACCATTT 0.676532 -284 GTTTCACACCTTTTGACTCTTCAC 12 24 0 CACACCTTTT 0.942728 -14 ACACGCCTCTTACGAGTGCTT 34 290 0 CACGCCTCTT 0.953033 -11 TGATTTGCTTCACATCTTTTTACGTCGTAC 36 234 1 CACATCTTTT 0.656571 -67 TTAACACACCTTTATGACAGTCAG 40 5 1 CACACCTTTA 0.873116 -296 TACTTACCGGAACACCTTTACCC 41 190 1 AACACCTTTA 0.444202 -13 CGACCATCGTCACGCCTTTTGTCTGCAGAA 46 147 0 CACGCCTTTT 0.968357 -154 TGCGCATGATAACGCCTTTTAGGGGCAATT 47 175 1 AACGCCTTTT 0.780426 -126 GTTTGTTTTTCACGCGCTTTACAGCCCGAA 49 123 1 CACGCGCTTT 0.735128 -73 ********** Masking position 2 Map Score: 5.69727 Number of sites scoring better than the average of aligned sites = 315 Number in coding regions = 274 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 12 TGATGAAAACGCAGGCTGTTTTTGCAAGAC 6 88 0 GCAGGCTGTT 0.937284 -97 ACAAGCGACAGCGGGCTGAATGGTGGTTAA 14 121 0 GCGGGCTGAA 0.875679 -81 ATCCAAAGTTTCGGGCTGTTATGTTTTAAT 19 41 1 TCGGGCTGTT 0.966374 -115 TCGGAACATTTCAGGCTGTAGCCAACGTAG 20 23 1 TCAGGCTGTA 0.936331 -60 TCGTCATCTTTCAGGCTGTAACTACGTTGG 20 44 0 TCAGGCTGTA 0.936331 -39 CGTTCGCCCTTCGGGCCGTTGCTGGCGCAA 32 86 0 TCGGGCCGTT 0.870376 -195 ACTTTCCTGATCTGGCTGATTGCATACCAA 38 29 1 TCTGGCTGAT 0.668439 -66 AATATGATGAGCAGGCTGCTCATCCAGAAA 40 201 0 GCAGGCTGCT 0.821381 -100 TCCGGCCTTTTCGGGCTGTAAAGCGCGTGA 49 132 0 TCGGGCTGTA 0.958892 -64 ********** Masking position 6 Map Score: 4.57319 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 150 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 13 GTATGTTAATTGCAGTCATGCTTCACACCG 2 14 0 TGCAGTCATG 0.924503 -287 TTTATGTGTCTGCAGGCATCTTTCCATTCA 7 182 0 TGCAGGCATC 0.881154 -119 TCATTTAAAGCGCAGTAATGGCGATAATTT 9 92 1 CGCAGTAATG 0.785543 -30 CGGTATTAACCGCAGGCACCAGGAAGGATA 32 53 1 CGCAGGCACC 0.840905 -228 AGCCACCTCTTGCAGTCATCTTTTCTTCGC 37 41 1 TGCAGTCATC 0.93815 -36 TCGCGCAGTCCTGGTTAAAGAGG 41 4 1 CGCAGTCCTG 0.897223 -199 CTGCTCTCGCCGCAATCATGATATGCCATT 44 102 1 CGCAATCATG 0.880346 -199 GTCCGCATAACGCAATCATCGCACCTTTCC 48 131 0 CGCAATCATC 0.901121 -170 TGCTCCCACTCGCAGTCATCCTCCCTCACT 50 224 1 CGCAGTCATC 0.97885 -59 ********** Masking position 4 Map Score: 3.58493 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 219 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 14 ACCAAATATCGTTATTATCACTCCCTTTTACT 4 109 0 GTTATTTCCT 0.766282 -192 ACTCCTTAACGTTATTGTCTCTGCTACTGATA 15 16 1 GTTATTTCCT 0.766282 -220 CCTTAGAGATGTTATCTTTACTTGCTTCGAAG 27 103 0 GTTATCTTCT 0.842554 -69 CTGGCGCAACGTTATCCTTCCTGGTGCCTGCG 32 63 0 GTTATCTTCT 0.842554 -218 ACGTCAGTGAGTCATCCTCCCGGATGCACCAT 32 113 1 GTCATCTCCG 0.950272 -168 TTGTTTATCGCTCATCGTCGCTGCGTGGCGCA 34 250 0 CTCATCTCCT 0.922383 -51 ACCTCTTGCAGTCATCTTTTCTTCGCTCTATC 37 45 1 GTCATCTTCT 0.926143 -32 TCGGTGGGAAGTCATCATCTCTTAGTATCTTA 48 169 1 GTCATCTCCT 0.977994 -132 GCATCTGGTTCTCATCATCGCGTAATATTGAT 48 239 1 CTCATCTCCG 0.83633 -62 CCCACTCGCAGTCATCCTCCCTCACTCCTGCC 50 228 1 GTCATCTCCT 0.977994 -55 ****** ** ** Masking position 5 Map Score: 4.6303 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 127 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 15 CTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGT 1 66 1 CGCAACGTTC 0.930372 -235 ATCTCCAGAATGCCGCCGTTTGCCAGAAATTCG 1 194 1 TGCCGCGTTC 0.895705 -107 ATTTACTCGTTGTCATCGATACCGTAATCGCCA 2 227 1 TGTCACGTAC 0.430171 -74 TGGCTGGATGTGCAACCGGCTTCTTCACTTATC 3 86 1 TGCAACGCTC 0.963516 -181 GCTCCAGTATTGCCAGCGCCTGCGCTTCATCTT 3 237 0 TGCCACGCTC 0.964172 -30 AAATATTCAACGCCATCGACTTTTTATGCCTTT 17 30 0 CGCCACGCTT 0.58989 -136 GAAATCCCTACGCAAACGTTTTCTTTTTCTGTT 17 95 1 CGCAACGTTC 0.930372 -71 AAGGGGTAGATGCAATCGGTTACGCTCTGTATA 25 94 1 TGCAACGTTC 0.966706 -68 TACATCTCACTGCAAAAGACTTCGAAGCAAGTA 27 84 1 TGCAAAGCTC 0.754138 -88 TTGTGGTTGGTGTAATCGGTTTCAGTTGTGATG 36 23 0 TGTAACGTTC 0.882727 -278 ATCACATCAGTGTAATCGCTTACACTAACATTT 36 205 0 TGTAACGTTC 0.882727 -96 TCCAGAATGCTGCAAACGTCTCTGCGAGACAAA 44 234 0 TGCAACGCTT 0.754138 -67 AGAGTCCCTTTGTGATCGCTTTCACGGAGCATA 47 35 1 TGTGACGTTC 0.637506 -266 AGAAGAAGGATGCCGCAGGTTTCATCAATATTA 48 261 0 TGCCGAGTTC 0.499369 -40 ***** ** ** * Masking position 8 Map Score: 4.71363 Number of sites scoring better than the average of aligned sites = 674 Number in coding regions = 622 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392